Genetic diagnostic yield in an 11-year cohort of craniosynostosis patients

Craniosynostosis may present in isolation, 'non-syndromic', or with additional congenital anomalies/neurodevelopmental disorders, 'syndromic'. Clinical focus shifted from confirming classical syndromic cases to offering genetic testing to all craniosynostosis patients. This retrospective study assesses diagnostic yield of molecular testing by investigating prevalences of chromosomal and monogenic (likely) pathogenic variants in an 11-year cohort of 1020 craniosynostosis patients. 502 children underwent genetic testing. Pathogenic variants were identified in 174 patients (35%). Diagnostic yield was significantly higher in syndromic craniosynostosis (62%) than in non-syndromic craniosynostosis (6%). Before whole exome sequencing (WES) emerged, single-gene testing was performed using Sanger sequencing or multiplex ligation-dependent probe amplification (MLPA). Diagnostic yield was 11% and was highest for EFNB1, FGFR2, FGFR3, and IL11RA. Diagnostic yield for copy number variant analysis using microarray was 8%. From 2015 onwards, the WES craniosynostosis panel was implemented, with a yield of 10%. In unsolved, mainly syndromic, cases suspected of a genetic cause, additional WES panels (multiple congenital anomalies (MCA)/intellectual disability (ID)) or open exome analysis were performed with an 18% diagnostic yield. To conclude, microarray and the WES craniosynostosis panel are key to identifying pathogenic variants. in craniosynostosis patients. Given the advances in genetic diagnostics, we should look beyond the scope of the WES craniosynostosis panel and consider extensive genetic diagnostics (e.g. open exome sequencing, whole genome sequencing, RNA sequencing and episignature analysis) if no diagnosis is obtained through microarray and/or WES craniosynostosis panel. If parents are uncomfortable with more extensive diagnostics, MCA or ID panels may be considered.

The International X-Linked Hypophosphatemia (XLH) Registry: first interim analysis of baseline demographic, genetic and clinical data

BACKGROUND

X-linked hypophosphatemia (XLH) is a rare, hereditary, progressive, renal phosphate-wasting disorder characterized by a pathological increase in FGF23 concentration and activity. Due to its rarity, diagnosis may be delayed, which can adversely affect outcomes. As a chronic disease resulting in progressive accumulation of musculoskeletal manifestations, it is important to understand the natural history of XLH over the patient's lifetime and the impact of drug treatments and other interventions. This multicentre, international patient registry (International XLH Registry) was established to address the paucity of these data. Here we present the findings of the first interim analysis of the registry.

RESULTS

The International XLH Registry was initiated in August 2017 and includes participants of all ages diagnosed with XLH, regardless of their treatment and management. At the database lock for this first interim analysis (29 March 2021), 579 participants had entered the registry before 30 November 2020 and are included in the analysis (360 children [62.2%], 217 adults [37.5%] and 2 whose ages were not recorded [0.3%]; 64.2% were female). Family history data were available for 319/345 (92.5%) children and 145/187 (77.5%) adults; 62.1% had biological parents affected by XLH. Genetic testing data were available for 341 (94.7%) children and 203 (93.5%) adults; 370/546 (67.8%) had genetic test results; 331/370 (89.5%) had a confirmed PHEX mutation. A notably longer time to diagnosis was observed in adults ≥ 50 years of age (mean [median] duration 9.4 [2.0] years) versus all adults (3.7 [0.1] years) and children (1.0 [0.2] years). Participants presented with normal weight, shorter length or height and elevated body mass index (approximately - 2 and + 2 Z-scores, respectively) versus the general population. Clinical histories were collected for 349 participants (239 children and 110 adults). General data trends for prevalence of bone, dental, renal and joint conditions in all participants were aligned with expectations for a typical population of people with XLH.

CONCLUSION

The data collected within the International XLH Registry, the largest XLH registry to date, provide substantial information to address the paucity of natural history data, starting with demographic, family history, genetic testing, diagnosis, auxology and baseline data on clinical presentation.

Topical injection of sclerosant to treat cheek subcutaneous venous malformation resulting in blindness: a case report

Loss of vision after topical injection of sclerosant is a rare and uncommon complication. We describe a case with vision loss following the facial injections of physician-compounded (PCP) foam sclerotherapy which was created by room air. A 3-year-old boy underwent injection of 5ml polidocanol foamed with room air to treat the venous malformation on the cheek near the left orbit. The boy experienced the whole facial swelling on day 2 after the third injection, especially involving the left side, the visual acuity in the left eye was counting fingers at 30 cm and the swelling reduced at 7 days later after referral. Fundus examination on day 15 revealed hemorrhage inferior to the optic disc and fluorescein angiography revealed blocked fluorescein. The OCT on day 15 showed the edema of the nerve fiber layer beside the fovea. The patient's hearing was also impaired. PCP foam sclerotherapy with room air produced in typical concentrations, preparations as well as volumes always causes vision loss among children. Continued evaluation on the effects of product, gas, volume, and patient age identify optimal approaches will avoid the toxicity and side-effects caused by facial foam sclerotherapy.

Data saves lives: optimising routinely collected clinical data for rare disease research

Necessity driven organisational change in the post-pandemic landscape has seen health care providers adopting innovations to manage and process health data. These include the use of 'real-world' datasets of routinely collected clinical information, enabling data-driven delivery. Rare disease risks being 'left-behind' unless our clinical and research communities engage with the challenges and opportunities afforded by the burgeoning field of health data informatics. We address the challenges to the meaningful use and reuse of rare disease data, and, through a series of recommendations around workforce education, harmonisation of taxonomy, and ensuring an inclusive health data environment, we highlight the role that those who manage rare disease must play in addressing them.

Together4RD position statement on collaboration between European reference networks and industry

Notwithstanding two decades of policy and legislation in Europe, aimed to foster research and development in rare conditions, only 5-6% of rare diseases have dedicated treatments. Given with the huge number of conditions classed as rare (which is increasing all the time), this equates to major unmet need for patients (over 30 million in the EU alone). Worryingly, the pace of Research and Innovation in Europe is lagging behind other regions of the world, and a seismic shift in the way in which research is planned and delivered is required, in order to remain competitive and-most importantly-bring meaningful, disease-altering treatments to those who desperately need them. The European Reference Networks (ERNs), launched in 2017, hold major potential to alleviate many of these challenges, and more, but only if adequately supported (financially, technically, and via robust policies and infrastructure) to realise that potential: and even then, only if able to forge robust collaborations harnessing the expertise, resources, knowledge and data of all stakeholders involved in rare disease, including Industry. To-date, however, ERN-Industry interactions have been largely limited, for a range of reasons (concerning barriers both tangible and perceived). This Position Statement analyses these barriers, and explains how Together4RD is seeking to move the needle here, by learning from case studies, exploring frameworks for collaboration, and launching pilots to explore how best to plan and deliver multistakeholder interactions addressing real research needs.

Leigh syndrome global patient registry: uniting patients and researchers worldwide

BACKGROUND

Leigh Syndrome (LS) is a rare genetic neurometabolic disorder, that leads to the degeneration of the central nervous system and subsequently, early death. LS can be caused by over 80 mutations in mitochondrial or nuclear DNA. Patient registries are important for many reasons, such as studying the natural history of the disease, improving the quality of care, and understanding the healthcare burden. For rare diseases, patient registries are significantly important as patient numbers are small, and funding is limited. Cure Mito Foundation started a global patient registry for LS in September 2021 to identify and learn about the LS patient population, facilitate clinical trial recruitment, and unite international patients and researchers. Priorities were to allow researchers and industry partners to access data at no cost through a clear and transparent process, active patient engagement, and sharing of results back to the community.

RESULTS

Patient registry platform, survey design, data analysis process, and patient recruitment strategies are described. Reported results include demographics, diagnostic information, symptom history, loss of milestones, disease management, healthcare utilization, quality of life, and caregiver burden for 116 participants. Results show a high disease burden, but a relatively short time to diagnosis. Despite the challenges faced by families impacted by Leigh syndrome, participants, in general, are described as having a good quality of life and caregivers are overall resilient, while also reporting a significant amount of stress.

CONCLUSION

This registry provides a straightforward, no-cost mechanism for data sharing and contacting patients for clinical trials or research participation, which is important given the recruitment challenges for clinical trials for rare diseases. This is the first publication to present results from a global patient registry for Leigh Syndrome, with details on a variety of patient-specific and caregiver outcomes reported for the first time. Additionally, this registry is the first for any mitochondrial disease with nearly 70% of participants residing outside of the United States. Future efforts include continued publication of results and further collaboration with patients, industry partners, and researchers.

Cross-national comparative study of orphan drug policies in Saudi Arabia, the United States, and the European Union

Background

Rare diseases are chronic, serious, and life-threatening conditions that have not received sufficient attention from drug developers due to their rarity. Policies have been implemented to encourage research and incentivize the development of orphan drugs. However, the implementation of these policies has been inconsistent worldwide.

Objective

The primary aim of this study was to compare orphan drug policies in the United States, Europe, and Saudi Arabia (SA) and assess their impact on the number of approved indications.

Method

Lists of all drugs granted orphan designations and authorized for marketing in the United States, European Union, and SA were extracted using orphan drug lists available in regulatory body databases. The availability of these drugs, regarding their approval for orphan indication and designation, was assessed and classified using Anatomical Therapeutic Chemical codes.

Result

A total of 792 orphan drug designations with at least one authorized indication were identified in this study. Of these, 92% were designated by the Food and Drug Administration (FDA), and 27% were designated by the European Medicine Agency (EMA). The FDA, EMA, and Saudi Food and Drug Authority approved 753, 435, and 253 orphan drugs, respectively.

Conclusion

Fewer orphan drug approvals were found in SA than in the United States and Europe. This highlights the need to focus on rare diseases and orphan drugs and for policies to be created in SA to attract pharmaceutical markets and fulfill unmet orphan drug approval needs.

Development and testing of methods to record and follow up spells in patients with alternating hemiplegia of childhood

BACKGROUND

Developing methods to record Alternating Hemiplegia of Childhood (AHC) spells is essential for clinical trials and patient care.

OBJECTIVES

Test the following hypotheses: 1) Video-library training improves participants' ability to correctly identify AHC spells. 2) A custom-designed event-calendar with weekly reviews results in consistent documentation of such events over time. 3) Use of an electronic diary (e-Diary) to register events is a useful tool.

METHODS

1) A video-library of AHC type spells was developed along with specific training; the effect of the training was tested in 36 caregivers. 2) An event-calendar was similarly developed and provided to 5 caregivers with weekly videoconference meetings for 8 weeks. 3) An e-Diary was developed and offered to 33 patients; time of usage and caregivers' feedback (telephone interview) were analyzed.

RESULTS

1) Video-library training: Wilcoxon test showed improvement in caregiver identification of spells (p = 0.047), Cohen's Kappa demonstrated high degree of agreement between caregivers'-experts' classifications (>0.9). 2) Event-calendar: 96.42% of entries had complete information; this did not change during follow up (p = 0.804). 3) e-Diary: whereas 52% of respondents used the e-Diary when offered (duration: 10.5 ± 8.1 months), 96.3% indicated they would use it in future studies. Those who used it for 13 months, were very likely to use it during the rest of that year.

CONCLUSIONS

Video-library training improved spell identification. Calendar with weekly reviews resulted in a sustained and consistent record keeping. Caregivers' e-Diary feedback was encouraging with long-term usage in many. These approaches could be helpful for AHC and, potentially, in similar disorders.

Clinical, genetic, and structural characterization of a novel TUBB4B tubulinopathy

Microtubules are cytoskeletal polymers of ⍺/β-tubulin heterodimers essential for a wide range of cellular processes. Pathogenic variations in microtubule-encoding genes (e.g., TUBB4B, which encodes the β-4B tubulin isotype) are responsible for a wide spectrum of cerebral malformations, collectively referred to as "tubulinopathies." The phenotypic manifestation of TUBB4B-associated tubulinopathy is Leber congenital amaurosis with early-onset deafness (LCAEOD), an autosomal dominant syndrome characterized by photoreceptor and cochlear cell loss; all known patients have pathogenic variations in amino acid R391. We present the clinical and molecular genetics findings of a 16-year-old female with a de novo missense variant in exon 1 of TUBB4B, c.32 A > G (p.Gln11Arg; Q11R). In addition to hearing loss and hyperopia without retinal abnormalities, our proband presented with two phenotypes of unknown genetic etiology, i.e., renal tubular Fanconi Syndrome (FS) and hypophosphatemic rickets (HR). The Q11R variant expands the genetic basis of early sensory hearing loss; its consequences with respect to microtubule structure are described. A mechanistic explanation for the FS and rickets, involving microtubule-mediated translocation of transporter proteins to and from the apical membrane of renal proximal tubular cells, is proposed.

DPH1 and DPH2 variants that confer susceptibility to diphthamide deficiency syndrome in human cells and yeast models

The autosomal-recessive diphthamide deficiency syndrome presents as intellectual disability with developmental abnormalities, seizures, craniofacial and additional morphological phenotypes. It is caused by reduced activity of proteins that synthesize diphthamide on human translation elongation factor 2. Diphthamide synthesis requires seven proteins (DPH1-DPH7), with clinical deficiency described for DPH1, DPH2 and DPH5. A limited set of variant alleles from syndromic patients has been functionally analyzed, but databases (gnomAD) list additional so far uncharacterized variants in human DPH1 and DPH2. Because DPH enzymes are conserved among eukaryotes, their functionality can be assessed in yeast and mammalian cells. Our experimental assessment of known and uncharacterized DPH1 and DPH2 missense alleles showed that six variants are tolerated despite inter-species conservation. Ten additional human DPH1 (G113R, A114T, H132P, H132R, S136R, C137F, L138P, Y152C, S221P, H240R) and two DPH2 (H105P, C341Y) variants showed reduced functionality and hence are deficiency-susceptibility alleles. Some variants locate close to the active enzyme center and may affect catalysis, while others may impact on enzyme activation. In sum, our study has identified functionally compromised alleles of DPH1 and DPH2 genes that likely cause diphthamide deficiency syndrome.

RDKG-115: Assisting drug repurposing and discovery for rare diseases by trimodal knowledge graph embedding

Rare diseases (RDs) may affect individuals in small numbers, but they have a significant impact on a global scale. Accurate diagnosis of RDs is challenging, and there is a severe lack of drugs available for treatment. Pharmaceutical companies have shown a preference for drug repurposing from existing drugs developed for other diseases due to the high investment, high risk, and long cycle involved in RD drug development. Compared to traditional approaches, knowledge graph embedding (KGE) based methods are more efficient and convenient, as they treat drug repurposing as a link prediction task. KGE models allow for the enrichment of existing knowledge by incorporating multimodal information from various sources. In this study, we constructed RDKG-115, a rare disease knowledge graph involving 115 RDs, composed of 35,643 entities, 25 relations, and 5,539,839 refined triplets, based on 372,384 high-quality literature and 4 biomedical datasets: DRKG, Pathway Commons, PharmKG, and PMapp. Subsequently, we developed a trimodal KGE model containing structure, category, and description embeddings using reverse-hyperplane projection. We utilized this model to infer 4199 reliable new inferred triplets from RDKG-115. Finally, we calculated potential drugs and small molecules for each of the 115 RDs, taking multiple sclerosis as a case study. This study provides a paradigm for large-scale screening of drug repurposing and discovery for RDs, which will speed up the drug development process and ultimately benefit patients with RDs. The source code and data are available at https://github.com/ZhuChaoY/RDKG-115.

Prevalence of Mental Health Problems, Associated Factors, and Health-Related Quality of Life in Children with Long-Gap Esophageal Atresia in Sweden

BACKGROUND

Children with long-gap esophageal atresia (LGEA) face a high risk of digestive and respiratory morbidity, but their mental health outcomes have not been investigated. We aimed to identify the prevalence of mental health problems in children with LGEA, associated factors and health-related quality of life (HRQOL).

METHODS

Twenty-six children with LGEA aged 3-17 were recruited nationwide in Sweden. One of their parents and adolescents aged 11-17 completed information on the child's mental health (Strength and Difficulties Questionnaire), generic (PedsQL 4.0) and condition-specific HRQOL (EA-QOL). Parents gave information on current child symptomatology. Mental health level was determined using validated norms; abnormal≥90 percentile/borderline≥80 percentile/normal. Elevated levels were considered borderline/abnormal. Data were analyzed using descriptives, correlation and Mann-Whitney-U test. Significance level was p < 0.05.

RESULTS

Twelve children with LGEA aged 3-17 (46%) had elevated scores of ≥1 mental health domain in parent-reports, whereas 2 adolescents (15%) in self-reports. In parent-reports, 31% of the children had elevated levels of peer relationship problems, with associated factors being child sex male (p = 0.037), airway infections (p = 0.002) and disturbed night sleep (p = 0.025). Similarly, 31% showed elevated levels of hyperactivity/inattention, and associated factors were male sex (p = 0.005), asthma (p = 0.028) and disturbed night sleep (p = 0.036). Elevated levels of emotional symptoms, seen in 20%, were related to swallowing difficulties (p = 0.038) and vomiting problems (p = 0.045). Mental health problems correlated negatively with many HRQOL domains (p < 0.05).

CONCLUSIONS

Children with LGEA risk mental health difficulties according to parent-reports, especially peer relationship problems and hyperactivity/inattention, with main risk factors being male sex, airway problems and sleep disturbances. This should be considered in follow-up care and research, particularly since their mental health problems may impair HRQOL.

LEVELS OF EVIDENCE

Prognosis study, LEVEL II.

Meta-analysis of the diagnostic and clinical utility of exome and genome sequencing in pediatric and adult patients with rare diseases across diverse populations

PURPOSE

This meta-analysis aims to compare the diagnostic and clinical utility of exome sequencing (ES) vs genome sequencing (GS) in pediatric and adult patients with rare diseases across diverse populations.

METHODS

A meta-analysis was conducted to identify studies from 2011 to 2021.

RESULTS

One hundred sixty-one studies across 31 countries/regions were eligible, featuring 50,417 probands of diverse populations. Diagnostic rates of ES (0.38, 95% CI 0.36-0.40) and GS (0.34, 95% CI 0.30-0.38) were similar (P = .1). Within-cohort comparison illustrated 1.2-times odds of diagnosis by GS over ES (95% CI 0.79-1.83, P = .38). GS studies discovered a higher range of novel genes than ES studies; yet, the rate of variant of unknown significance did not differ (P = .78). Among high-quality studies, clinical utility of GS (0.77, 95% CI 0.64-0.90) was higher than that of ES (0.44, 95% CI 0.30-0.58) (P < .01).

CONCLUSION

This meta-analysis provides an important update to demonstrate the similar diagnostic rates between ES and GS and the higher clinical utility of GS over ES. With the newly published recommendations for clinical interpretation of variants found in noncoding regions of the genome and the trend of decreasing variant of unknown significance and GS cost, it is expected that GS will be more widely used in clinical settings.

Composite endpoints, including patient reported outcomes, in rare diseases

BACKGROUND

When assessing the efficacy of a treatment in any clinical trial, it is recommended by the International Conference on Harmonisation to select a single meaningful endpoint. However, a single endpoint is often not sufficient to reflect the full clinical benefit of a treatment in multifaceted diseases, which is often the case in rare diseases. Therefore, the use of a combination of several clinically meaningful outcomes is preferred. Many methodologies that allow for combining outcomes in a so-called composite endpoint are however limited in a number of ways, not in the least in the number and type of outcomes that can be combined and in the poor small-sample properties. Moreover, patient reported outcomes, such as quality of life, often cannot be integrated in a composite analysis, in spite of their intrinsic value.

RESULTS

Recently, a class of non-parametric generalized pairwise comparisons tests have been proposed, which members do allow for any number and type of outcomes, including patient reported outcomes. The class enjoys good small-sample properties. Moreover, this very flexible class of methods allows for prioritizing the outcomes by clinical severity, allows for matched designs and for adding a threshold of clinical relevance. Our aim is to introduce the generalized pairwise comparison ideas and concepts for rare disease clinical trial analysis, and demonstrate their benefit in a post-hoc analysis of a small-sample trial in epidermolysis bullosa. More precisely, we will include a patient relevant outcome (Quality of life), in a composite endpoint. This publication is part of the European Joint Programme on Rare Diseases (EJP RD) series on innovative methodologies for rare diseases clinical trials, which is based on the webinars presented within the educational activity of EJP RD. This publication covers the webinar topic on composite endpoints in rare diseases and includes participants' response to a questionnaire on this topic.

CONCLUSIONS

Generalized pairwise comparisons is a promising statistical methodology for evaluating any type of composite endpoints in rare disease trials and may allow a better evaluation of therapy efficacy including patients reported outcomes in addition to outcomes related to the diseases signs and symptoms.

Proposal of a new clinical entity: Paraprotein negative IL-1 mediated inflammatory dermatosis (PANID) that may precede Schnitzler syndrome

Schnitzler syndrome (SchS) is an autoinflammatory disease that is defined by the presence of 2 obligate criteria; an IgM or IgG monoclonal paraprotein and a chronic urticarial rash. Typically, there is an excellent clinical response to IL-1 antagonism. There are reports in the literature of a variant type of SchS that does not fulfil the 2 obligate criteria but responds to IL-1 blockade. Equally, there are reports of an urticarial rash preceding the development of a paraprotein by several years. We describe 3 cases in this manuscript. The first fits the Strasbourg diagnostic criteria of SchS, Simon and Asli (2013); however, with several decades of diagnostic delay. The second case at initial presentation did not fit the major criteria for SchS; however, later developed a monoclonal IgM. Finally we report, a third case that has not yet been confirmed to have a monoclonal IgM/IgG at the time of writing despite 12 years of symptoms and in whom a somatic autoinflammatory disorder remains within the differential. All cases responded strikingly to anakinra, an IL-1 receptor blocker. We propose a new clinical entity, paraprotein negative IL-1 mediated inflammatory dermatosis (PANID), that may act as a precursor or risk factor for the development of SchS or other autoinflammatory conditions.

Congenital disorders of glycosylation: narration of a story through its patents

Congenital disorders of glycosylation are a group of more than 160 rare genetic defects in protein and lipid glycosylation. Since the first clinical report in 1980 of PMM2-CDG, the most common CDG worldwide, research made great strides, but nearly all of them are still missing a cure. CDG diagnosis has been at a rapid pace since the introduction of whole-exome/whole-genome sequencing as a diagnostic tool. Here, we retrace the history of CDG by analyzing all the patents associated with the topic. To this end, we explored the Espacenet database, extracted a list of patents, and then divided them into three major groups: (1) Drugs/therapeutic approaches for CDG, (2) Drug delivery tools for CDG, (3) Diagnostic tools for CDG. Despite the enormous scientific progress experienced in the last 30 years, diagnostic tools, drugs, and biomarkers are still urgently needed.

Overcoming challenges in rare disease registry integration using the semantic web - a clinical research perspective

The growing number of disease-specific patient registries for rare diseases has highlighted the need for registry interoperability and data linkage, leading to large-scale rare disease data integration projects using Semantic Web based solutions. These technologies may be difficult to grasp for rare disease experts, leading to limited involvement by domain expertise in the data integration process. Here, we propose a data integration framework starting from the perspective of the clinical researcher, allowing for purposeful rare disease registry integration driven by clinical research questions.

Patient-reported outcomes in Gaucher's disease: a systematic review

BACKGROUND

Gaucher's disease (GD), a rare condition, represents the most common lysosomal storage disorder. The cardinal manifestations of GD are fatigue, hepatosplenomegaly, anemia, thrombocytopenia, bone pain, and bone infarction, thereby culminating in a marked deterioration of patients' quality of life (QoL). Patient-reported outcomes (PROs) offer valuable insights into the impact of GD on patients' QoL and symptoms. This systematic review aimed to identify and analyze PROs and outcome measures in GD patients.

METHODS

We systematically searched PubMed, Web of Science Core Collections, EMBASE, SCOPUS, Cochrane Library, PsycINFO, Wan Fang Data, China National Knowledge Infrastructure (CNKI), and the Chinese Biomedical Literature Database (CBM). The methodological quality of the included studies was assessed using a mixed methods assessment tool.

RESULTS

A total of 33 studies were identified, encompassing 24 distinct patient-reported outcome instruments, with the most frequently employed instrument being the SF-36. The study designs included eighteen cross-sectional studies, seven pre- and post-intervention investigations, three randomized controlled trials, two cohort studies, two qualitative inquiries, and one validation study. These studies explored diverse domains such as the QoL and cardinal symptoms (e.g., fatigue, pain, bleeding, cognition, social relationships, and psychological functioning) in patients with GD. Furthermore, significant attention was directed towards the appraisal of the therapeutic benefits of various interventions in patients with GD. A novel GD-specific instrument has also been developed, which has two applied versions: a 24-item variant for routine clinical monitoring and a 17-item form for use in clinical trials.

CONCLUSION

PROs have garnered increased attention and concern in the realm of GD. Despite this progress, it is noteworthy that the instruments used to measure PROs in GD are still predominantly generic instruments. While researchers have endeavored to develop and validate a disease-specific instrument, currently the use of this instrument is limited. Owing to several challenges, including the small number of patients, heterogeneity of the disease, and cross-regional discrepancies in study findings, GD poses substantial difficulties in the measurement of QoL and development of instruments. Consequently, patients with GD require more dependable measurement instruments that accurately reflect their QoL, efficacy of treatment, and facilitate healthcare decision-making.

Rare disease variant curation from literature: assessing gaps with creatine transport deficiency in focus

BACKGROUND

Approximately 4-8% of the world suffers from a rare disease. Rare diseases are often difficult to diagnose, and many do not have approved therapies. Genetic sequencing has the potential to shorten the current diagnostic process, increase mechanistic understanding, and facilitate research on therapeutic approaches but is limited by the difficulty of novel variant pathogenicity interpretation and the communication of known causative variants. It is unknown how many published rare disease variants are currently accessible in the public domain.

RESULTS

This study investigated the translation of knowledge of variants reported in published manuscripts to publicly accessible variant databases. Variants, symptoms, biochemical assay results, and protein function from literature on the SLC6A8 gene associated with X-linked Creatine Transporter Deficiency (CTD) were curated and reported as a highly annotated dataset of variants with clinical context and functional details. Variants were harmonized, their availability in existing variant databases was analyzed and pathogenicity assignments were compared with impact algorithm predictions. 24% of the pathogenic variants found in PubMed articles were not captured in any database used in this analysis while only 65% of the published variants received an accurate pathogenicity prediction from at least one impact prediction algorithm.

CONCLUSIONS

Despite being published in the literature, pathogenicity data on patient variants may remain inaccessible for genetic diagnosis, therapeutic target identification, mechanistic understanding, or hypothesis generation. Clinical and functional details presented in the literature are important to make pathogenicity assessments. Impact predictions remain imperfect but are improving, especially for single nucleotide exonic variants, however such predictions are less accurate or unavailable for intronic and multi-nucleotide variants. Developing text mining workflows that use natural language processing for identifying diseases, genes and variants, along with impact prediction algorithms and integrating with details on clinical phenotypes and functional assessments might be a promising approach to scale literature mining of variants and assigning correct pathogenicity. The curated variants list created by this effort includes context details to improve any such efforts on variant curation for rare diseases.

Epidemiological research on rare diseases using large-scale online search queries and reported case data

BACKGROUND

Rare diseases have become a major public health concern worldwide. However, detailed epidemiological data are lacking. With the development of the Internet, search queries have played an important role in disease surveillance. In this study, we explored a new method for the epidemiological research on rare diseases, using large-scale online search queries and reported case data. We distilled search logs related to rare diseases nationwide from 2016 to 2019. The case data were obtained from China's national database of rare diseases during the same period.

RESULTS

A total of 120 rare diseases were included in this study. From 2016 to 2019, the number of patients with rare diseases estimated using search data and those obtained from the case database showed an increasing trend. Rare diseases can be ranked by the number of search estimated patients and reported patients, and the rankings of each disease in both search and reported case data were generally stable. Furthermore, the disease rankings in the search data were relatively consistent with the reported case data in each year, with more than 50% of rare diseases having a ranking difference of -20 to 20 between the two systems. In addition, the relationship between the disease rankings in the two systems was generally stable over time. Based on the relationship between the disease rankings in the search and reported case data, rare diseases can be classified into two categories.

CONCLUSION

Online search queries may provide an important new resource for detecting rare diseases. Rare diseases can be classified into two categories to guide different epidemiological research strategies.

Schooling experiences in children with long-gap esophageal atresia compared with children with esophageal atresia and primary anastomosis: a Swedish study

BACKGROUND

Children with long-gap esophageal atresia (LGEA) risk living with aerodigestive morbidity and mental health difficulties. No previous study has investigated their experiences of schooling, despite the importance of schools in children's development, learning and social relationships. We aimed to describe experiences of schooling in children with LGEA in Sweden in comparison with children with EA who had primary anastomosis.

METHOD

Children with LGEA aged 3-17 were recruited nationwide in Sweden. One parent completed a survey on their child's school-based supports (according to definitions from the Swedish National Agency for Education), school absence, school satisfaction, school functioning (PedsQL 4.0), mental health (Strength and Difficulties Questionnaire) and current symptomatology. School data were compared between 26 children with LGEA to that from 95 children with EA who had PA, a hypothesized milder affected group. Mental health level was determined using validated norms; abnormal ≥ 90 percentile. Data were analyzed using descriptives, correlation and Mann-Whitney-U test. Significance level was p < 0.05.

RESULTS

Formal school-based support was reported in 17 (65.4%) children with LGEA and concerned support with nutritional intake (60%), education (50%) and medical/special health needs (35%). The prevalence of school-based support was significantly higher compared to children with PA overall (36.8%, p = 0.013) and regarding nutritional intake support (20%, p < 0.001). In children with LGEA, school-based support was related to low birth weight (p = 0.036), young child age (p = 0.014), height ≤ -2SD for age/sex (p = 0.024) and an increased number of aerodigestive symptoms (p < 0.05). All children with LGEA who had abnormal mental health scores had school-based support, except for one child. Nine children with LGEA (36%) had school absence ≥ 1times/month the past year, more frequently because of colds/airway infections (p = 0.045) and GI-specific problems compared to PA (p = 0.003). School functioning scores were not significantly different from children with PA (p = 0.34) but correlated negatively with school-based support (< 0.001) and school absence (p = 0.002). One parent out of 26 reported their child's school satisfaction as "not good".

CONCLUSIONS

Children with LGEA commonly receive school-based support, reflecting multifaceted daily needs and disease severity. School absence is frequent and related to poorer school functioning. Future research focusing on academic achievement in children with EA is needed.

Critical assessment of variant prioritization methods for rare disease diagnosis within the Rare Genomes Project

Background

A major obstacle faced by rare disease families is obtaining a genetic diagnosis. The average "diagnostic odyssey" lasts over five years, and causal variants are identified in under 50%. The Rare Genomes Project (RGP) is a direct-to-participant research study on the utility of genome sequencing (GS) for diagnosis and gene discovery. Families are consented for sharing of sequence and phenotype data with researchers, allowing development of a Critical Assessment of Genome Interpretation (CAGI) community challenge, placing variant prioritization models head-to-head in a real-life clinical diagnostic setting.

Methods

Predictors were provided a dataset of phenotype terms and variant calls from GS of 175 RGP individuals (65 families), including 35 solved training set families, with causal variants specified, and 30 test set families (14 solved, 16 unsolved). The challenge tasked teams with identifying the causal variants in as many test set families as possible. Ranked variant predictions were submitted with estimated probability of causal relationship (EPCR) values. Model performance was determined by two metrics, a weighted score based on rank position of true positive causal variants and maximum F-measure, based on precision and recall of causal variants across EPCR thresholds.

Results

Sixteen teams submitted predictions from 52 models, some with manual review incorporated. Top performing teams recalled the causal variants in up to 13 of 14 solved families by prioritizing high quality variant calls that were rare, predicted deleterious, segregating correctly, and consistent with reported phenotype. In unsolved families, newly discovered diagnostic variants were returned to two families following confirmatory RNA sequencing, and two prioritized novel disease gene candidates were entered into Matchmaker Exchange. In one example, RNA sequencing demonstrated aberrant splicing due to a deep intronic indel in ASNS, identified in trans with a frameshift variant, in an unsolved proband with phenotype overlap with asparagine synthetase deficiency.

Conclusions

By objective assessment of variant predictions, we provide insights into current state-of-the-art algorithms and platforms for genome sequencing analysis for rare disease diagnosis and explore areas for future optimization. Identification of diagnostic variants in unsolved families promotes synergy between researchers with clinical and computational expertise as a means of advancing the field of clinical genome interpretation.

Improving Detection of Alpha-1 Antitrypsin Deficiency: Role of the Allergist

Alpha-1 antitrypsin deficiency (AATD) is a genetic disorder that manifests as lung and/or liver disease. Because symptoms of AATD overlap with those of common pulmonary and hepatic conditions, AATD is often misdiagnosed, which has resulted in substantial underdiagnosis of AATD worldwide. Although screening patients for AATD is recommended, the lack of procedures to facilitate testing remains a barrier to accurate diagnosis of AATD. Delays in AATD diagnosis can worsen outcomes for patients by postponing appropriate disease-modifying treatments. Patients with AATD-related lung disease experience symptoms similar to other obstructive lung disorders and are often misdiagnosed for years. In addition to existing screening guidelines, we recommend that screening for AATD become a standard part of allergists' workups of patients with asthma and fixed obstructive disease, chronic obstructive pulmonary disease, bronchiectasis without known origin, and patients under consideration for treatment with biologics. This Rostrum article reviews screening and diagnostic tests available in the United States and emphasizes evidence-based strategies to increase testing frequency and improve AATD detection rates. We underscore the pivotal role of allergists in managing care for patients with AATD. Finally, we urge health care providers to be aware of potentially poor clinical outcomes among patients with AATD during the coronavirus disease 2019 pandemic.

Cardiovascular risk in rare diseases: a prognostic stratification model in a cohort of sarcoidosis patients

Sarcoidosis is a rare granulomatous disease that can affect any organ; as other chronic diseases, it leads to increased risk of atherosclerosis and cardiovascular (CV) disease. The aim of our observational study was to define a prognostic stratification model of sarcoidosis patients based on the evaluation of CV risk through common carotid Doppler ultrasound and cardiovascular risk scores assessment; for this reason, a clinical phenotyping of sarcoidosis patients in four subgroups was done, based on the different organ involvement. A cohort of 53 sarcoidosis patients and a cohort of 48 healthy volunteers were enrolled. Results showed that CV risk was higher in sarcoidosis cohort than in the control group when evaluated through CV risk scores and Doppler parameters: peak-systolic velocity (PSV) and end-diastolic velocity (EDV) were significantly lower in sarcoidosis cohort (p = 0.045 and p = 0.017, respectively), whereas intima media thickness (IMT) showed higher values in sarcoidosis group than in controls (p = 0.016). The analysis of sarcoidosis phenotypes showed no significative differences of CV risk among them when CV risk scores were considered, while partial differences emerged by evaluating subclinical atherosclerosis. Results also highlighted a relationship between CV risk score and carotid Doppler ultrasound parameters: EDV showed an inverse correlation with Framingham score (R = - 0.275, p = 0.004), whereas IMT showed a direct one (R = 0.429; p = 0.001); furthermore, an inverse correlation between PSV and EDV and illness duration (R = - 0.298, p = 0.030 and R = - 0.406, p = 0.002, respectively) was found, so suggesting a higher CV risk in patients with a longer story of disease.

Quality of life of Brazilian families who have children with Fragile X syndrome: a descriptive study

This study aimed to assess the Family Quality of Life (FQoL) of Brazilian families with male children with Fragile X syndrome (FXS). Data from 53 families were collected using forms that included sociodemographic and clinical information, as well as the Beach Center Family Quality of Life Scale, a 5-point Likert scale ranging from "very dissatisfied" (1) to "very satisfied" (5). The mean overall FQoL score was 3.56 ± 0.79; the emotional well-being domain had the lowest score (2.98 ± 1.11) and showed significant differences between the other domains: family interaction (3.81 ± 0.89; p < 0.001), parenting (3.66 ± 0.89; p < 0.001), physical and material well-being (3.48 ± 0.83; p < 0.001), and disability-related support (3.75 ± 0.98; p < 0.001). Physical and material well-being was the second-lowest domain and was statistically different from the family interaction domain (p = 0.013). Lower FQoL satisfaction ratings were found in families with children who had difficulty getting along with people of the same age (t(51) = -3.193, p = 0.002; d = 1.019) and difficulty in living together on a day-to-day basis (t(51) = -3.060, p = 0.004; d = 0.888). These results highlight the importance of proper emotional support for the family, emphasizing the need to provide assistance not only for individuals with FXS but also for other family members. Besides, we advocate for the adoption of public policies that provide financial assistance to families and the implementation of the Brazilian Policy of Comprehensive Care for People with Rare Diseases.